Mercurial > repos > greg > vsnp_statistics
annotate vsnp_statistics.xml @ 14:ce1f889b3340 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 02 Aug 2021 21:13:19 +0000 |
| parents | 1becb6606626 |
| children | 44b07199be73 |
| rev | line source |
|---|---|
| 7 | 1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@"> |
| 0 | 2 <description></description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 0 | 6 <requirements> |
| 8 | 7 <expand macro="biopython_requirement"/> |
| 8 <expand macro="numpy_requirement"/> | |
| 9 <expand macro="openpyxl_requirement"/> | |
| 10 <expand macro="pandas_requirement"/> | |
| 11 <expand macro="xlrd_requirement"/> | |
| 0 | 12 </requirements> |
| 13 <command detect_errors="exit_code"><![CDATA[ | |
| 14 #import re | |
| 4 | 15 |
| 8 | 16 #if $input_type_cond.input_type in ["single", "pair"]: |
| 17 #set read1 = $input_type_cond.read1 | |
| 0 | 18 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
| 4 | 19 ln -s '${read1}' '${read1_identifier}' && |
| 8 | 20 #if $input_type_cond.input_type == "pair": |
| 21 #set read2 = $input_type_cond.read2 | |
| 4 | 22 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) |
| 23 ln -s '${read2}' '${read2_identifier}' && | |
| 0 | 24 #else: |
| 8 | 25 #set read2 = None |
| 0 | 26 #end if |
| 27 #else: | |
| 8 | 28 #set read1 = $input_type_cond.reads_collection['forward'] |
| 14 | 29 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
| 8 | 30 ln -s '${read1}' '${read1_identifier}' && |
| 31 #set read2 = $input_type_cond.reads_collection['reverse'] | |
| 14 | 32 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) |
| 8 | 33 ln -s '${read2}' '${read2_identifier}' && |
| 0 | 34 #end if |
| 4 | 35 |
| 0 | 36 python '$__tool_directory__/vsnp_statistics.py' |
| 8 | 37 --read1 '${read1_identifier}' |
| 38 #if $read2 is not None | |
| 39 --read2 '${read2_identifier}' | |
| 0 | 40 #end if |
| 8 | 41 #if $read1.is_of_type('fastqsanger.gz'): |
| 42 --gzipped | |
| 43 #end if | |
| 44 --dbkey '$samtools_idxstats.metadata.dbkey' | |
| 45 --samtools_idxstats '$samtools_idxstats' | |
| 46 --vsnp_azc_metrics '$vsnp_azc_metrics' | |
| 1 | 47 --output '$output' |
| 0 | 48 ]]></command> |
| 49 <inputs> | |
| 50 <conditional name="input_type_cond"> | |
| 51 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
| 8 | 52 <option value="single" selected="true">Single files</option> |
| 53 <option value="paired">Paired reads</option> | |
| 54 <option value="pair">Paired reads in separate data sets</option> | |
| 0 | 55 </param> |
| 8 | 56 <when value="single"> |
| 57 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
| 4 | 58 </when> |
| 8 | 59 <when value="paired"> |
| 60 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> | |
| 61 </when> | |
| 62 <when value="pair"> | |
| 63 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
| 64 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> | |
| 0 | 65 </when> |
| 66 </conditional> | |
| 8 | 67 <param name="samtools_idxstats" type="data" format="tabular" label="Samtools idxstats file"/> |
| 68 <param name="vsnp_azc_metrics" type="data" format="tabular" label="vSNP: add zero coverage metrics file"/> | |
| 0 | 69 </inputs> |
| 70 <outputs> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
71 <data name="output" format="tabular"/> |
| 0 | 72 </outputs> |
| 73 <tests> | |
| 4 | 74 <!-- A single fastq file --> |
| 75 <test expect_num_outputs="1"> | |
| 8 | 76 <param name="input_type" value="single"/> |
| 4 | 77 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
| 78 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> | |
| 8 | 79 <param name="vsnp_azc_metrics" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
80 <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/> |
| 4 | 81 </test> |
| 82 <!-- A set of paired fastq files --> | |
| 83 <test expect_num_outputs="1"> | |
| 8 | 84 <param name="input_type" value="pair"/> |
| 0 | 85 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
| 86 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
| 4 | 87 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> |
| 8 | 88 <param name="vsnp_azc_metrics" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
89 <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/> |
| 4 | 90 </test> |
| 8 | 91 <!-- A collection of paired fastq files --> |
| 4 | 92 <test expect_num_outputs="1"> |
| 8 | 93 <param name="input_type" value="paired"/> |
| 4 | 94 <param name="reads_collection"> |
| 95 <collection type="paired"> | |
| 96 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
| 97 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
| 98 </collection> | |
| 99 </param> | |
| 8 | 100 <param name="samtools_idxstats" value="samtools_idxstats5.tabular" ftype="tabular" dbkey="89"/> |
| 101 <param name="vsnp_azc_metrics" value="add_zc_metrics5.tabular" ftype="tabular" dbkey="89"/> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
102 <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/> |
| 0 | 103 </test> |
| 104 </tests> | |
| 105 <help> | |
| 106 **What it does** | |
| 107 | |
| 4 | 108 Accepts associated fastq files, SAMtools idxstats files and **vSNP: add zero coverage** metrics files and extracts information from them |
| 8 | 109 to produce an Excel spreadsheet containing statistics for each sample. The samples can be a single read, a single set of paired reads in |
| 110 separate datasets or collection of paired reads. The output statistics include reference, file size, mean read length, mean read quality, | |
| 4 | 111 reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, reference with coverage, average depth |
| 112 of coverage and good SNP count. | |
| 0 | 113 </help> |
| 4 | 114 <expand macro="citations"/> |
| 0 | 115 </tool> |
| 116 |